links
Link to section 'Introduction' of 'links' Introduction
LINKS is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.
BioContainers: https://biocontainers.pro/tools/links
Home page: https://github.com/bcgsc/LINKS
Link to section 'Versions' of 'links' Versions
- 2.0.1
Link to section 'Commands' of 'links' Commands
- LINKS
Link to section 'Module' of 'links' Module
You can load the modules by:
module load biocontainers
module load links
Link to section 'Example job' of 'links' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run links on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=links
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers links